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Detailed information for vg1002718424:

Variant ID: vg1002718424 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2718424
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGCGGCCACGCGGAACGGCCCGTCGGCGTCGGCGTCGTCGTCGTCGCAGATCAGCGTGGCGTTGCATCGGATGGAGTGATGGAGATGGAGTCGTTTATG[G/A]
GATGCCGCCTTGACGAGGCAGCGCTTGCCGGTGATGGGGTTGTAGACGAGGAAGTAGCAGGAGAATCTGCAGCAGCCGAGCAGGACGCGGCCGCCGCGGC

Reverse complement sequence

GCCGCGGCGGCCGCGTCCTGCTCGGCTGCTGCAGATTCTCCTGCTACTTCCTCGTCTACAACCCCATCACCGGCAAGCGCTGCCTCGTCAAGGCGGCATC[C/T]
CATAAACGACTCCATCTCCATCACTCCATCCGATGCAACGCCACGCTGATCTGCGACGACGACGACGCCGACGCCGACGGGCCGTTCCGCGTGGCCGCCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.50% 6.50% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 80.80% 19.20% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 69.40% 30.60% 0.00% 0.00% NA
Tropical Japonica  504 95.60% 4.40% 0.00% 0.00% NA
Japonica Intermediate  241 86.30% 13.70% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1002718424 G -> A LOC_Os10g05500.1 synonymous_variant ; p.Ser158Ser; LOW synonymous_codon Average:73.758; most accessible tissue: Zhenshan97 young leaf, score: 90.078 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002718424 NA 1.22E-07 mr1062 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1002718424 NA 3.75E-06 mr1210 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1002718424 NA 7.52E-06 mr1305 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1002718424 2.08E-06 2.07E-06 mr1736 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1002718424 NA 4.45E-06 mr1736 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1002718424 NA 2.41E-06 mr1765 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1002718424 NA 2.29E-07 mr1585_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1002718424 NA 1.74E-06 mr1585_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251